Even if a writer is avoiding science fiction, the modern age has seriously affected cultural notions of magic, be they mutant powers or deity/demon granted.
Powers and Special Abilities often seem to be "spiritual programs" in human beings. They can be added, removed, or copied without physiological change, and they're all "encoded" in the same way, so a device or person that can steal, detect or otherwise interact with "powers" will work on any superhuman, regardless of where their abilities come from. In video games, these abilities often use "MP" the same way a computer uses electricity.
Thus, if you need to increase your powers fast, just look around for an Upgrade Artifact! Forget about rolling your own powers, however — the tools required to create the programmed powers in the first place (such as a programming language and associated compiler program) are nowhere to be found, and nobody ever thinks to ask about them. Compare Vancian Magic and Power Copying. A subtrope is Discard and Draw, where the "diskspace" freed by losing one power gets utilized for another power afterwards. For powers that are performed through actual programming with mathematics, see Formulaic Magic.
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This is the core concept behind magic in the Lyrical Nanoha franchise. Several of the characters are in fact considered to be programs, namely Reinforce and the Wolkenritter. In fact, the catchphrase which Nanoha uses to transform ends with "Set Up!" The fluff, however, tones it down somewhat, explaining that magical programs/spells cannot be copied arbitrarily and each mage has a highly personalized library of spells. They can share the principle of their respective spells (cf. generic algorithms) but each spell is its caster's personal implementation and often an upgrade of an older spell from their library.
Although Reinforce cancopy the spells of anyone who has had their linker core drained by the Book of Darkness, but that's a unique ability that only she possesses.
In Ah! My Goddess, powers are programs, the universe is a great computer, Heaven is where the sysops work, and the greatest threat to reality is a well-written virus. Amusingly, errors manifest as actual bugs and are fixed by whacking them with a mallet.
In Psyren, PSI abilities, especially Burst-types, can be programmed by the user to work unconsciously or preform tasks more complicated then what the Psychicer could do on their own.
In Code Geass, Geass powers apparently cannot be copied or transferred per se, but the "Code" — a power package of immortality, immunity to Geass, vaguely-defined psionic facilities, and Super Empowering — can be transferred to a Geass user at the cost of stripping them of their original Geass. C.C.'s initial goal is to find someone to pass her powers to, so that she could die.
In Angel Beats!, this is how Tenshi gets her powers, but in a twist, it's actually a program. This is a plot point.
Kinnikuman had a Devil Chojin named Stecase King. A walking cassette player/walkman who could obtain the fighting skills of other Chojin by switching out his cassette tapes. This eventually backfired because his tapes of Kinnikuman himself were badly outdated, leaving Stecase King with the Crouching Moron before he got the Hidden Badass.
In Jojo's Bizarre Adventure Part 6, main villain Enrico Pucci's original Stand power "White Snake" allows him to extract (among other things) the Stand of its victim into a "disc". The discs are physical objects that can be handled by anyone, and swapped around.
Digimon Tamers treats this sort of literally. Cards from the Digimon card game can be slashed through a Digivice to temporarily load its effects onto one's partner Digimon, which are themselves programs; in the context of the card game, such cards are also programs. Additionally, killing a Digimon and loading its data enables one to use the attacks of that Digimon.
In Medaka Box, not only are powers freely tradable (assuming you have someone with the power to trade them, of course) there's a character with the power to create other powers and give them to people. You just need to ask what you want.
Played with by Devil Fruits in One Piece. taking just one bite instantly gives you the power, and renders the fruit powerless. However, some do have physical changes, there is literally no way to remove them, and trying to eat a second one apparently causes a very nasty and fatal backfire.
Powers in Yamada-kun and the Seven Witches can all apparently be copied. Though of course, only one can be stored at a time, and it's overwritten by the next power if another power is copied.
The trope is common in Comic Book superhero worlds like The DCU and Marvel Universe. Marvel's Rogue, for example, can take others powers, either temporarily or permanently. There are other "borrowers" (such as Parasite from The DCU) and "copiers" (such as Mimic from the Marvel Universe) throughout both. There's even some Green Rocks on the DC side: Pre Crisis "Gold Kryptonite" could permanently rob Kryptonians of their powers and render them just like humans.
The character Sage from the Marvel Universe really stands out for this trope. Via her Awesome by Analysis powers she is able to jump-start, overclock, alter or even trigger mutant abilities.
Not counting Rogue, mentioned above, whose power as mentioned above is explicitly this), the X-Men's most egregious single victim of this trope is Psylocke. She started as a out as a telepath and precog and subsequently gone through so many power changes that her abilities seem to literally be gained or lost Depending on the Writer, sometimes without even a Hand Wave explanation.
Rogue herself takes it to a new level. She doesn't just borrow powers, but knowledge and skills as well. Everyone she's ever touched stays in there, and it's driven her to near madness before. However, she's also had all those past powers activated at once before (Sage did it, natch), sending her into one-woman army territory. It doesn't happen often because of the danger of losing herself (and the fact that she'd be a Game Breaker) but it's awesome to behold when it does.
Also the other side of the coin where devices or artifacts that render superhumans powerless apparently work on ALL superhumans, regardless of their type of powers or the origin of them. DC is worse about this than Marvel; Marvel usually just applies this to mutants, who get their powers from a particular genetic strand and could thus (at least with comic science) reasonably be repressed, but DC tends to have the same power-dampening collars work on (for example) Superman and Wonder Woman, despite the vast difference in the way their powers work and the source of them.
This was subverted in Kurt Busiek's arc in Action Comics, where an intergalactic Auctioneer kidnaps a bunch of heroes with the intent of selling them to collectors. On his ship, everyone lost their powers. Superman figured that since everyone's powers came from different sources, that they were being blocked mentally. He breaks the block by putting himself in mortal danger (for a normal human) and is protected by his invulnerability. Since he knows it's a lie, the mental block is broken.
Not that Marvel is innocent of this: anyone up in arms about the Juggernaut being a mutant in the movieverse, an assumption based on Leech's ability to depower him, should remember that in the comics, Leech has been able to depower Inhumans (offshoot of humanity empowered by the local Green Rocks' mist), the Power Pack (kids whose powers were transferred to them by an alien whose species is born with powers), and Spider-Man as well as mutants. Whether it'd work on Iron Man or someone else whose powers are externally-based remains to be seen.
One wonders what would happen to beings that are mutants, but not superpowered, like the Ninja Turtles. Though I guess they are superpowered, by turtle standards.
In the Marvel universe, they're called 'Mutates.' A mutant is born with it; a mutate is someone who has been altered.
Marvel Comics also has S.P.I.N. technology, Super Power inhibiting nanobots that can strip seemingly any super of their powers. They were used during the after math of the Civil War arc. Which seemed to work on Mutants, Mutates and Gamma Mutates to various degrees. And of course some genius sent amateurs to use them on Spider-Man, it ends how you think it would. Unknown how the S.P.I.N. tech would work on martial arts based powers like Iron Fist's.
Though S.P.I.N. did tend to avert this at first. The nanites had to be specifically designed for the intended victim, and wouldn't work on anyone else (unless they had the same power etc). Eventually, generic ones were developed, but these only covered common powers rather than everything (Spider-Man got stung with them once - he lost his strength & agility, but kept his spider-sense) and were temporary in effect, which fit better.
Peter Petrelli owes a lot to Mimic. Mimic can take on the powers of any mutant he's around, his body altering itself to match (such as gaining Beast's physique and Angel's wings). The villainous main Marvel Universe one has permanently taken on the powers of the original X-Men in addition to gaining new ones based on who he's around. The good Exiles version can hold any five powers at once. At one point, Exile!Mimic mimics the Phoenix Force from one of the Summers - granted, as with all his mimics he got it at half power, but he mimic'ed a fundamental force of the universe (and half of infinity is still infinity).
Anthony "Tony" Masters, aka Taskmaster falls into this, as he can copy every muscle fiber twitch of most people's physical abilities (He can throw a shield like Cap, Punch like Iron Fist, but don't ask him to jump like Hulk) from simply watching it of this as just like a computer his mind gets full, so his brain has formatted itself to dump memories even those of his wife and past life as an Ex-shield agent, which is how he met his wife. It gets even sadder as Avengers Academy member Finesse believes she may be his daughter due to her having similar abilities, meaning she's possibly gonna have this weakness. He admits when they meet alone that he can't remember but it's a possibility. He won't take a DNA test, though, as he likes to stay off the grid.Avengers Academy #23 has a possible future version of Finesse, and her memory has been affected so much, that as she looks at her daughter, she can only remember her vaguely by her movements.
One aspect/flaw of his abilities is that he's only able to replay (and to an extent, integrate) moves but not expand or tweak them to his own needs (depending). For instance, he can punch at superhuman speeds by watching a video on fast-forward but can not simply punch at superhuman speeds just because he wants to (not to mention, he explicitly says he doesn't do this often anyway since being an otherwise normal human, superhuman feats destroy his body from stress and strain).
Averted in one storyline, where for several issues, the kids' powers are swapped around. The skills are individual, and they all have fits learning how to use the powers they're not familiar with, and come up with individual applications of the new powers.
A literal example of Powers as Programs: the DC supervillain Prometheus, who uses a helmet that allows him to download other people's physical skills and knowledge for his own use (he can't duplicate superpowers, though). Hilariously, Batman defeats him by overwriting his fighting skills with the physical skills of Stephen Hawking.
Black Alice (real name Lori Manning) is basically the Dark Magical Girl version of Rogue. She's an Anti-Hero (or Hero or Anti-Villain depending on the story) who can temporarily steal any magic user's powers and use them as well as they can. She doesn't even have to be near them; Zatanna could be halfway across the world and Black Alice could still steal her powers. Lori has even managed to steal two magic users' powers at once. Perhaps realizing all of this made her too close to a God-Mode Sue, the writers also saddled her with depression (severe enough to warrant medication) and a Nerf thanks to the Reign In Hell event.
The Super Friends version of Black Alice (from the latest comic book iteration) only copies magical abilities, rather than stealing them.
JLA: Act of God relies on this as its premise; a mysterious event removes superpowers from all the characters in the DCU albeit inconsistently. Humanoid Aliens like Superman and Martian Manhunter lost abilities that are typical of their species (i.e., they don't actually have "superpowers" per se) beyond that of baseline humans. Technology is supposed to remain functional so Steel's Powered Armor is unimpeded, but somehow Kyle Rayner's ring (made with Oan technology) no longer works. Yeah, it really made no sense at all.
Films — Live Action
In The Matrix, skills are literal computer programs, and any of the rebels at any time can call Mission Control, ask for a program, and receive instant powers.
The film Space Jam has a bunch of aliens using technology to steal the basketball talents from NBA stars.
This arises as a temporary side effect of the Silver Surfer's energy aura on the Fantastic Four in the movie sequel Rise of the Silver Surfer. Whenever Johnny touches one of the other heroes, they swap powers with him (this somehow even includes instantly transforming Ben back into his human form). Near the end, Johnny ends up copying all their powers to face down Doctor Doom with their combined might.
In My Super Ex-Girlfriend, the eponymous superhero initially absorbed her powers from a meteorite. This very meteorite is also the key to taking her powers away again to be transferred to another character
Dark City treats memories this way; Dr. Screber mixes them in a lab and injects them into the forehead using a syringe.
Magic in The Dragon Knight books involves creating a computer-code-like statement in your mind. In fact, Jim is particularly good at clever use of spells because of his passing knowledge of computer programming.
In Brian Lumley's book Necroscope, the villain, Boris Dragosani, has the ability to read the memories of the dead. This also allows him to steal and learn the powers of the super-powered dead, which means that he gets pretty Badass by the end of the book.
The protagonist, Harry Keogh, also has this ability. Unlike Dragosani, Keogh learns from the dead by asking nicely. This also gives him the "power" of having the nearby dead rise from their graves to serve up a Deus ex Machina With Cheese.
This is one of the central ideas behind Joan Vinge's Snow Queen/Summer Queen books. When the "mystical sybil" begins her "incantation" with "Input!" and ends it with "No further analysis!" you can pretty much guess what's going on with the "magic" here.
The Speech in the Young Wizards universe is essentially a programing language for reality; spells are instructions and/or equations in The Speech and wizards are like the IT staff for the Universe who "know the little noises it makes every day when it's running. And where to kick it to make them stop."
The Trope Codifier and original source material for the Mega Ten video game series, Digital Devil Story, featured the Demon Summoning Program which did exactly what its name says. There is also the Demon Transfer Theory, which allows demons to use modems to move around the world.
Slightly varied in Alan Dean Foster's Cyber War, where a Navajo sandpainting grants 20th century detectives natural language command level access to Reality's core AI.
In the canonical Babylon 5 Techno-Mage trilogy by Jeanne Cavelos, the origin and use of Techno-Mage powers is gone into in some detail. Their powers are literally programs, though in a language unique to each Mage. This makes certain Mages adept at certain types of spells that other Mages find very difficult or even impossible, and means that Mages can develop specific spells that other Mages cannot use. Galen from Crusade has a very mathematical spell language, which enables him to break down spells into simpler and simpler terms which ultimately allows him to determine the basic origin of the Techno-Mages' powers and interface directly with his technology. The down side is that complex spells require complex equations, which are harder for him to visualise. Elric, his teacher, uses a completely different spell language based on visual imagery, but whilst this makes him extremely powerful he explicitly states that he could never have discovered the "root terms" needed to tap directly into his tech as his spell language doesn't work that way. Other Techno-Mage spell languages include sounds, dance and knitting patterns.
In Julian May's Saga of the Exiles and Galactic Milieu series, a lot of metapsychic stunts, performed both by a single and several characters, are literally called "programs" and can be shared, optimized and even booby-trapped.
Live Action TV
In Smallville, Clark Kent has lost his powers so many times, the wiki has a page for it. Naturally, as the comics section stated, it generally makes no sense.
He also temporarily transferred them to Eric Summers, twice, and Lana Lang.
But there is something even worse in season six to eight. Chloe Sullivan gains Empathic Healing from kryptonite exposure. When Brainiac uses a Mind Probe on her, it somehow gives her Super Intelligence and removed her healing power. It is never explained. It is also mentioned in Cure that Chloe has a large amount of kryptonite around her heart, which causes it to make even less sense since Brainiac obviously didn't remove that.
Common plot device in Charmed where some demon or warlock/evil witch is stealing other people's powers.
They even go so far as to have a group of demons who spend their time trading powers like trading cards... (though that could well be Lampshade Hanging). Another episode had demons using powers as currency for an auction over souls.
Not to mention that one episode revolved around the sisters accidentally swapping powers. A later episode had them use the same spell, but they accidentally ended up going into two random passersby.
Cole managed to absorb enough powers by hanging out in the demon afterlife and taking the power of every one that died that he broke out, loaded down with a ludicrous number of abilities.
This isn't even limited by the type of supernatural being. For example, in "Love Hurts", Prue swaps powers with a Darklighter (named Alec and played by Michael Trucco) and Piper swaps powers with the resident Whitelighter, Leo.
Arthur Petrelli also makes use of this trope, instantly stealing all powers from a target by touching them. Perhaps it runs in the family.
But Sylar isn't actually a Petrelli.
Nevertheless, it does run in Sylar's.
Dollhouse is all about this as a commercial business. Want a super-spy? Just programme one of the dolls.
Japan's Kamen Rider Decade. The title character and his similarly-powered rival (despite being from entirely seperate versions of Earth) use cards via their Transformation Trinkets to become/summon Riders from any past Kamen Rider series, perform special attacks, summon equipment, and make their finishing moves. The official descriptions of the suits and Transformation Trinkets even say that the cards are just stored data and that the suits have the power to read the data and alter reality in order to create things or change pre-existing things, as seen with their ability to turn past Riders into objects.
Kamen Rider Double is similar, possibly even justified. The main Transformation Trinkets are USB flash drive-like devices said to contain all the Earth's knowledge about a single subject (like magma), and come in two forms. The monster versions require a bio-connector port to be "injected" into the body with a special device that bonds the Memory to that user (though they can be passed around or used without a port, this is shown to be a bad idea). The Kamen Riders use more refined Memories that are apparently plug-and-play, as demonstrated when Double loans his Cyclone Memory to his ally Accel, who plugs it into his sword to beef it up with wind power (and the hypothetical CycloneAccel Xtreme implies that Accel's Memory can be used in Double's transformation belt rather than his specialized one).
The 13 RidersKamen Rider Ryuki special had Shinji get the Ryuki Advent Deck from the previous Ryuki, then at the end a dying Ren gives him his Knight deck when the Ryuki deck is broken.
The Rider Gears changing hands like this was practically the secondary gimmick in Kamen Rider Faiz.
Kamen Rider Fourze and his buddy Kamen Rider Meteor use devices called Astro Switches that plug into their belts. At different points in the show, Meteor borrows Fourze's elemental Switches, which let him perform burning or electrified punches and kicks. The Movie-exclusive Meteor Fusion form of Fourze plays this trope straighter, with Fourze gaining Meteor's mastery of Jeet Kun Do just by borrowing the Meteor Switch.
Kamen Rider Wizard has magic rings, which come in two distinct forms: Wizard Rings used by Wizard, the White Wizard, and Mage, and Beast Colors used by Beast. During one battle, Wizard ended up with one of Beast's rings and tried it out in a do-or-die moment; it worked, but had a slightly different effect. Beast, however, can't use Wizard's rings because they function differently note Wizard scans his rings over his belt, while Beast plugs them into a socket and uses them like keys. In a later episode, Wizard is given a ring and tries to use it, but his belt simply says "ERROR" - it turns out to be one of the White Wizard's rings.
In the non-canon direct-to-DVD joke episode, Wizard and Beast can indeed use each others' rings with exactly the same effects; however, this same DVD has Beast use his Buffalo ring on Wizard to make him sprout horns and a giant nose ring, so...
Superpowers granted by the storm can be transferred from one person to another by organ transplants.
Ecstacy causes powers to invert e.g. a girl with the ability to generate ice becomes a pyrokinetic for a while, and Curtis goes forward in time instead of backwards.
Seth is effectively a Power Disk Drive: he can absorb powers from people, store them in his body and then grant them to anyone else. So through him people can swap powers, lose powers or even gain multiple abilities.
In season 5, Finn gets a bad power that is later removed via a Power Nullifier. When Jess asks why he still has his telekinesis, he speculates that it must be Last In, First Out
On Haven, one of the Troubled has the ability to steal other people's Troubles, one at a time—he takes on the Trouble, the person who had it loses it, and then when he takes another Trouble the previous person gets theirs back.
The eponymous hero of Joe 90 acquires his abilities by having the "brain patterns" of specialists downloaded into his brain by a computer, via the electrodes in his glasses. The brain patterns are acquired by scanning their original owner's brains, either voluntarily or covertly, and recording them on tape to be stored until needed.
Numerous examples can be found in the Dungeons & Dragons game. Some specific monsters or magic treating Powers as Programs include:
A few magic spells (like "Contingency") allow the caster to attach other spells so they will trigger in specific circumstances automatically, without the mage's conscious decision.
A spell from 1E supplement Greyhawk Adventures, "Rary's Aptitude Appropriater", shortly gives the caster the use of someone else's non-weapon proficiency with the same level of skill. The proficiency isn't stolen, just duplicated.
The obliviax monster, or memory moss, can steal memories from the mind of humanoids, and even use their spells if attacked. The easiest way to regain the memories (and spells) is eating the obliviax (which is mildly poisonous).
A Blob Monster from the Fiend Folio, the enveloper, can use the spells and powers of the adventurers he'd devoured.
The "Jackal" wizard kit from The Complete Sha'ir's Handbook can cast no spell on his own, but steals spells directly from other mage's minds. (And let's not get into the Clockwork Mage, Digitalogist or Mageweaver kits...)
The Hierophant Prestige Class can pick a couple of special abilities that allow the transfer of either the Turn Undead power or Druid class features to another creature.
d20 Modern has spells you can literally send as emails, burn onto CD, or cast from a PDA.
Exalted represents nearly all powers as "charms", regardless of who has them; some charms allow you to copy others, while the Eclipse castes can (at a steep XP surcharge) learn the charms of anyone, regardless of power source. In a subversion of the usual rules, however, the compiler for new charms is available to most types of Exalt, who can freely invent new charms with enough time and experience.
It should be noted, however, that "regardless of power source" is somewhat disingenuous— all magic in the setting, and, for that matter, all everything in the setting, is essence based, essence being the metaphysical atomic structure of creation. Charms are simply specific patterns of essence run through a conscious soul — much like computer programs are specific patterns of electricity through a set of circuits.
Cosmic Encounters represents the racial advantages of each race in this fashion. Even though different powers are implied to come from from physiology, social structures, technology and so forth, there are cards and powers that can mimic, swap, or replace them all with ease.
In Phantasy Star Online, "Techniques" (the equivalent of spells) are explicitly gained from disks.
As is the case in Phantasy Star Universe. However, it is important to note that the Phantasy Star setting makes a distinction here. Techniques (or rather, TECHNICs), operate by allowing their user, with the aid of a technological/computerised focii and portable photon reactor, to manipulate energy fields by means of latent psychic abilities. This is not magic, but rather rooted in the setting's science. Magic did, at one point, exist in the Phantasy Star setting (See Rune and Kyra's Skills in Phantasy Star IV), but was mostly destroyed early in the continuity. Phantasy Star "Magic" made far less sense, was far more powerful, and far less predictable than TECHNICs, and did not behave like a computer program.
Phantasy Star IV had this in a more justified manner as well: Wren and Demi, both androids, can find spare parts in treasure chests at various points in the game and install them, gaining new abilities. Notable in that these weren't programs, but actual hardware components. (Demi, the female android and the more "human" of the two, actually asks the main character to avert his eyes while she performs this self-maintenance, as though she were undressing — the screen goes dark, and the player is treated to all manner of mechanical sound effects to indicate the complexity of the process.)
Various Final Fantasy games have played around with this in their magic and summoning systems:
Final Fantasy V had each of several "Jobs" represented by a crystal shard. When you picked up a shard, you got that class for your party. And then, after leveling up that Job suitably, you could equip one of its abilities or commands while in another Job.
Final Fantasy VI used literal Green Rocks called Magicite, magic from a dying Esper in crystallized form, as both a way to permanently learn spells and to summon the Esper it belonged to. Because these could be given to every character except the hidden characters, it was possible for most of your team to learn every spell in the game.
Final Fantasy VII used Materia of varying colors as a way to grant powers while attached to a character's equipment. Two very significant pieces of Materia would eventually drive the plot for the entire game. These Materia orbs were the only way to differentiate between characters' abilities, other than their Limit Breaks.
One part of the game has your materia being stolen, which severely limits your party as your stats drop heavily without materia and you have nothing to attack or heal with besides normal attacks and items.
Final Fantasy VIII allowed characters to 'junction' one or more beings called Guardian Forces to gain access to new menu commands. Like the Materia system in Final Fantasy VII, it is the only way to vary a character's abilities beyond their Limit techniques. Also, magic could be transferred between characters as easily as copying files from a CD.
Final Fantasy X has the so-called Sphere Grid which looks like a board game with substitutes for your characters on it. You can activate the fields on this grid with matching spheres and the character would immediately gain the status buff or magic spell from the field permanently.
Let's not forget the Blue Mage and Mimic classes. Blue Mages have the power to permanently use certain attacks after being hit by them (assuming they survive). Mimics have the ability to copy what ever attack was used immediately before their turn via the Mimic command.
Final Fantasy Tactics Advance allows units to learn skills by equipping weapons. After using the weapon enough, the skill is mastered, and the character will always be able to use this. The original Final Fantasy Tactics also had characters able to "equip" and un-equip action (job set) abilities and reaction and support abilities, although they were learned in a less explicitly "programmy" way.
The FFTA method is directly lifted from FFIX.
Final Fantasy X-2 also used this trope to the extreme, by allowing characters to switch classes via the use of Dressspheres, complete with a Magical Girl style Transformation Sequence. Switching between classes only used up a turn, and the party member could only use the moves related to that dresssphere. In some cases this is somewhat justified, (i.e. Not being able to use Warrior techniques while using the Gunner dresssphere). Other times it isn't, (magically losing the ability to sing when not wearing the Songstress dresssphere). Later on, you can acquire accessories and Grids that let you use abilities learned on one dressphere while equipped with another another.
The last one isn't that surprising, considering that the Songstress dresssphere is possessed by the spirit of Lenne, who could actually sing.
None of them are that surprising if you understand that the Dress Spheres are crystallized memories of someone's life and skills, meaning that each of the Dress Sphere's correspond to someone that was once alive and possessed the skills used by the cast. Oh, and yes, it is extremely similar to Materia, that isn't your imagination.
Seeing as how Nomura confirmed that VII and X take place in the same universe...
Players in The World Ends with You battle Noise with Psychs. These Psychs are activated via Pins. Normally, a player can activate a single Psych. Neku can use nearly all of them, even ones exclusive to Reapers. He just needs the appropriate pin. This leads to an interesting situation during a certain boss fight...
In the world of Shin Megami Tensei: Digital Devil Saga, the abilities used by your demonic alter-egos are literally programs, called 'Mantras', which you download from 'Karma Stations'. The game actually uses the term 'Download' directly. Of course, the fact that the whole thing is apparently a VR world effectively turns it into a sort of meta-self-referential-thingie. The Karma Stations being in the second game as well is one of your first clues that the 'real' world is also composed of data—data God begins deleting when it gets really pissed...
Another MegaTen game, Devil Survivor, makes use of a Demon Summoning Program much like described in the Digital Devil Story entry above. The program is based on music and functions like e-mail, with client programs on handheld computers (which need to be recharged) that communicate with a server. Oh, and you hire new demons by bidding on them over Ebay.
In later SMT and Persona games, demons or Personae will inherit skills learned from their predecessors; inheritance mechanics are more or less random, leading to the potential for hours of annoyance while fusing and re-fusing demons. This is not an inconvenience as of late, though, for Atlus has heard everyone's prayers and allowed the player to choose the moves the fusion result will learn in later games, starting with Devil Survivor, and the trend has continued with Devil Survivor 2, Persona 4: The Golden, and Shin Megami Tensei IV.
Speaking of Shin Megami Tensei IV, there's now the Demon Whisper mechanic, in which after a demon has learned all the moves it can learn as it is leveling up, it will talk to you and offer to teach you one of its moves, barring passive abilities and some seriously broken moves. You can even ask your demons to teach you the same move several times, increasing its effects or lowering its cost.
The first two Paper Mario games have a Badge system that works this way. Some Badges contain new moves for Mario's Hammer and Jump attacks. Others contain status buffs to Mario or his partners. Mario has a certain amount of "Badge Points" that limits the amount of Badges he can equip, as each Badge requires a certain amount of Badge Points to equip, but the player has the option to increase his Badge Points if he levels up.
Pokémon has the Technical Machines (TMs) and Hidden Machines (HMs). For goodness sake, the machines are literally discs from FireRed and LeafGreen on! While this makes sense for some technological Pokémon like Magnemite, it makes less sense that a CD could teach a rat how to spit lightning.
In FireRed and LeafGreen a cutscene appears when you teach a Pokémon a move by TM/HM in which you see the disc going directly to the Pokémon's head, and apparently force-feeding it the move.
There was a scene in a Pokémon manga where the TM used was a somewhat blocky-looking contraption that separated into two parts on each side of the Pokémon's head, and what were either sparkles or a spray came out to imbue the new move.
The same design also appears in the TCG. To make things more confusing, every item except TMs appear the same as it did in the TCG. The fact that the first appearance of TMs was a horribly broken set that was only released in Japan while the others are from the original set of cards may be a factor.
The video game characters in Captain Gamer are actually digitally created, with any special abilities just being part of their program. The title hero is thus capable of copying their signature abilities (Mario's jumping ability, Sonic's supersonic speed, and so on) by 'sharing data' with them, which is accomplished upon forming a bond of friendship.
In a way, the upgrading in System Shock is rather Powers as Programs styled. Justified because your character has been cybernetically enhanced and can thus use the terminals to enhance his body and mind.
Pretty much the same for TRON: Evolution, with older abilities being archived when upgraded into newer ones.
In Mega Man Battle Network the special powers aside from the Navis' basic attacks are all loaded onto oversized reusable microchips! Using them in combos to create more powerful attacks is even called a "Program Advance".
The "Navi Customizer" feature that debuted in the third game. You obtain these programs as you progress throughout the game and do events and you encode them into a special puzzle like interface, these parts either enhance Mega Man's abilities (like increasing the damage his Arm Cannon deals or how many chips you have available at the Custom screen) or alter some events like being guaranteed data chips from every battle (provided you can actually obtain chips from them normally) instead of a chance between it or some Zenny. You can even compress these programs a little via a cheat to help you fit them into the puzzle.
The "Soul Unison" in Network 5 and "Cross System" of Network 6 work in a similar way. Megaman "unites" with another Navi (after story events, of course), which temporarily grant him the special powers, strengths, and in some cases, weaknesses, of the other Navi (such as getting Protoman's shield). His armor changes color and design to reflect the change.
To be fair, everything is a program, since it does take place on the internet.
Used literally in Wild ARMs: Alter Code F. Professor Emma, now a playable character in this version, can "download" enemy special attacks by utilizing a special portable terminal that she carries around, then use the same terminal to execute any attack she's learned up to that point. This trope was also used in Wild ARMs 2 by Marivel, though it was more magical in nature rather than scientific.
This is how the skill system works in zOMG!. Since normal weapons don't work against the resident enemies, Gaians are forced to use special rings given to them by G-Corp Labtechs that augment their physical abilities and allow them to summon weapons of varying legitimacy to combat the animated threat. Of course it turns out that G-Corp isn't reallygiving out the rings in the first place...
Despite being changes to your genetics, Plasmid and gene tonics in BioShock can be installed, removed and reinstalled with ease. Then again, player characters seem to be the only people in Rapture who can withstand constant genetic alteration without going stark raving mad.
The Zone of the Enders Series plays this trope straight, considering that every Sub-Weapon you obtain must be acquired via 'downloading' it from either a conveniently placed terminal (ZOE) or via stealing the data from defeated units (The 2nd Runner)
Aside from the experimental Project Freelancer equipment seen in the story, Red vs. Blue gives us a literal example of powers as programs, in the form of the various AIs seen throughout the series. More often than not, the "powers" associated with the AIs are tied to a custom device found in their Freelancer agent's armor, but the Meta is able to instantly add them to his own armor without trouble.
The Humans in Gunnerkrigg Court have the etheric sciences, such as computers that allow to very literally use Powers as Programs. Explained here. In addition to giving each user a replica of Anja's own force shield and binding the troublesome fox-spirit, a few other handy effects were called by Donald in Chapter 37.
In The Inexplicable Adventures of Bob!, when Bob briefly gains super-powers, Fructose Riboflavin uses a machine to steal them. Bob kicks the machine's ray off-target, and his powers are transferred to a potted geranium instead. The flower becomes self-aware, thanks them, and flies off to explore the universe.
Magic in Unsounded exists as an energy field called the "khert", and the mages ("wrights", short for "spellwrights") who work with it are essentially supernatural programmers, recoding the fabric of reality to suit their whims according to a series of very specific rules. Thanks to a solid, consistent system and some excellent worldbuilding, the whole setup works beautifully.
Jane Doe is literally an identity thief. She steals the appearance, knowledge, memories, skills, and powers of anyone she touches.
Chinese hero Unity can copy the powers of any single other metahuman. As part of the forty-plus member People's Revolutionary Superhuman Collective (the largest superhero team on Earth), he's got a lot to choose from, and that doesn't include the villains he fights.
Prodigy has "photographic reflexes" and can mimic any athletic feat he witnesses.
Mexican hero Gideon copies powers, but has no choice about the target of is abilities. He copies the powers of whoever he is fighting.
Noiva de Salteador ("The Robber Bride" in Portuguese) is a Brazilian supervillain who can steal the powers of anyone she touches.
The villainous Paragon, another power mimic, is one of the most powerful beings in the Global Guardians PBEM Universe. Unlike most other power mimics, he copies the powers of ever other supervillain or hero within range (and his range is about half a mile) simultaneously... and the raw power of identical powers (superhuman strength, for example) stacks. And he can target trained supernormals as well.
In the Whateley Universe, there's an entire pile of Applied Phlebotinum to explain this stuff. The "science" of pattern theory is provided to explain how people with superpowers get enough energy to do the things they do, so people like Negator can block local powers, and people like Duplex or Thunderbird can mimic nearby powers. It's all explained by pattern theory.
Used nearly literally in an episode of Transformers Generation 1, in which Megatron used a device to transfer all the Decepticons' gimmick powers (including hardware-based ones, such as Starscream's null ray guns) to himself so he could defeat Optimus Prime in an honor duel. He won, obviously, and it took the Autobots half the episode to figure out that Megatron didn't usually teleport around when people took a shot at him.
One fan theory is that the Power Chip Rectifiers the Decepticon troops donated were something akin to access keys to subspace structures responsible for their assorted powers and ammo storage. The only reason Megatron can use most of them effectively is that he's focused, familiar with the effects and weapons in question, and a consummate warrior. And Optimus Prime was totally not expecting it. It may also be a short-range thing only - the donors in question were on the sidelines for the relevant fight scene.
The Transformers Animated version of Blackarachnia can steal powers from other Transformers a la X-Men's Rogue — hardware-based ones included.
In the Darkwing Duck episode "Jailbird", Negaduck steals the "Mystic Eye of Quackelcoatyl" and transfers the other villains' powers into himself. He even (accidentally) steals Joker-parody Quackerjack's "wackiness".
One episode of Tiny Toon Adventures featured "Batduck" being repeatedly laughed out of the "Just Us League" by all of the super-powered superheroes. When a Lex Luthor-pastiche steals all of their powers with a super vacuum cleaner for himself, Batduck accidentally saves the day by coming over again to try and brag about his greatness as a superhero, prompting the villain to try and absorb Batduck's "power"... and getting only Batduck's ego and incompetence.
ReBoot literally treats programs (or rather, commands) as powers: a Hide command makes one invisible, the Paint program becomes a veritable threat when it falls into the hands of an insane virus, and so on. This actually makes sense, as the people and the powers are all software. Bob literally downloads glitch into himself to gain Green Lantern Ring powers.
In Code Lyoko, the protagonists' powers really are programmed. Unfortunately for them, the show treats programming realistically, so any addition (even by the team's two Teen Geniuses) is a difficult and time-consuming task — and may as well induce "bugs" that need first to be worked out (as in episode "Triple Trouble"). On the other hand, XANA, being a superior Artificial Intelligence, can easily boost the heroes' powers — but since he's the Big Bad he reserves this for his mind-controlled puppets. Fortunately for them, what XANA can do from his end is limited by his own processing power. Things get kind of bad when he escapes to the internet, and they make him mad enough to create a nearly invincible monster that easily one-shots them.
Being derived from the result of a chemical fluke, The Powerpuff Girls are naturally this. The notion that their powers can be used by anyone is also employed, either when Mojo Jojo simply duplicates their powers onto himself or when Princess Morbucks uses Chemical X on herself to evolve identical powers.
In Ben 10 and its spinoffs, almost all "superpowered" characters that appear are actually members of distinct (sortof) alien species, with traits that are presumably normal to their species; however, the more impressive (and superhuman) traits are referred to as "powers", and can be suppressed, absorbed, stolen, switched, etc.
Subverted in the season 3 finale of My Little Pony: Friendship Is Magic, when the main cast gets their cutie marks swapped. Although their interests got swapped (Such as Pinkie Pie trying to buck apples and Applejack trying to make clothes), the actual talents didn't and they all suck hard at what they're trying to do. In fact, going back to their original talent is actually the key to reversing the spell.
In The Legend of Korra, a look into the past reveals that basal Energybending treats elemental bending as programs. Energybending can remove bending, give it back, and even replace it with a different element. The only reason humans can't bend multiple elements at once is because they lack the necessary energy. Avatars don't have this limitation because each one is a Fusion Dance between a human and the spirit Raava.